Preheat oven to 400° F. Line a large rimmed baking sheet with non-stick aluminum foil; lightly oil. Set aside.
Remove green caps of eggplant. Do not peel; cut into crosswise slices ⅜-inch thick. Lightly salt each side of eggplant slices (about 1 ½ teaspoons of salt) and place on paper towels. Let stand for 20 minutes; pat dry with paper towels. Arrange slices on oiled baking sheet; lightly brush with 1 tablespoon of olive oil. Sprinkle ½ teaspoon of oregano and ½ teaspoon of thyme on slices; cover with aluminum foil. Bake in preheated 400° F oven for 15 to 20 minutes, just until tender. Do not overcook. Remove from oven, and remove aluminum foil.
Reduce the oven temperature to 350° F.
Scrub the zucchini. Cut off the stem and bud ends, but do not peel. Cut lengthwise into 2-inch slices ⅜-inch thick. Salt the zucchini slices (about 1 ¼ teaspoons of salt) and place on paper towels. Let stand for 20 minutes; pat dry with paper towels. Heat 2 Tablespoons of olive oil in 12-inch skillet over medium heat. Working in batches, add zucchini slices; brown lightly on both sides, about 2 minutes per side. Remove to paper towels to drain.
In the same skillet that was used for the zucchini, sauté the onions until tender but not browned, about 7 minutes. Increase heat to medium high. Add the bell pepper slices and minced garlic. Cook for several minutes until fairly tender. Set aside ½-cup of the tomatoes. Add the rest of the tomatoes to the onion/bell pepper mixture and remaining ¼ teaspoon of salt. Cook over medium high heat until the tomatoes have rendered their juice and most of the juice has evaporated. Add additional salt if necessary.
Layer the ingredients as follows: (1) ⅓ of the onion/bell pepper/garlic/tomato mixture; (2) half of the zucchini; (3) ⅓ of the eggplant; (4) ⅓ of the onion/bell pepper, garlic, tomato mixture; (5) remaining zucchini; (6) half of the remaining eggplant; (7) remaining onion/bell pepper/garlic/tomato mixture; (8) remaining eggplant; and (9) reserved tomato. (See Tip 2)
Cover and heat in preheated 350° F oven for 25 to 30 minutes, or until mixture is heated through and bubbly. Yield: 6 to 8 servings. (See Tip 3)